Manager Call 2017-07-19

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Joining the Call on Zoom

https://stanford.zoom.us/j/754529609

Agenda

From June 21st Call

Annotation Qualifiers

  • What are the next steps?
    • Add guidelines to github documentation with examples for use of each BP qualifier (include positive and negative directionality)
    • Propose a half-day online working group meeting for this
      • acts_upstream_of_or_within
      • acts_upstream_of
      • involved_in
      • regulates
    • Decide on SOP for legacy annotations
      • This may be different for different annotation groups.
      • What would be involved in providing computational approaches to help curators?


Working groups management on GitHub

Pascale has created new ‘Projects’ from the action items that proposed working groups at the GOC meeting, see https://github.com/orgs/geneontology/projects It would be nice to have a project lead on each of these, and add any relevant ticket.

We need to prioritize and probably add additional working groups.


Process to deal with stale annotations

Draft message: Dear GO contributors,

GO is now using GitHub as a tracking system for ontology changes and for annotation issues. The repository can be found here: https://github.com/geneontology UPDATE to ???

We need to have a contact person for each group, ideally registered to GitHub, or at least an email address where we can address queries. The list of current contacts is here: https://github.com/geneontology/go-ontology/blob/master/curator_group_contacts.tsv

UPDATE to ???

The contact person(s) is (are) responsible for (1) answering requests regarding the annotations provided by the group (2) providing feedback on ontology if the ontology editors would like the expertise of that group


Right now we have no contacts persons for the following groups:

  • CACAO (Suzi Aleksander, TAMU)
  • DFLAT (Donna Slonim, see http://dflat.cs.tufts.edu/index.htm)
  • EcoCyc (Ingrid Keseler, SRI)
  • EcoliWiki (Jim Hu, TAMU)
  • Ensembl (Maria Martin, EBI)
  • EnsemblFungi (Maria Martin, EBI)
  • EnsemblPlants (Maria Martin, EBI)
  • GDB (Ulrike Boehme, Sanger ?)
  • GR (Pankaj)
  • HPA (Emma Lundberg) emma.lundberg at scilifelab.se
  • JCVI (no contact, project has ended)
  • LIFEdb (Rainer Pepperkok Pascale contacted 07/19/2017)
  • MENGO (Michelle Gwinn)
  • MTBBASE (Fiona McCarthy)
  • NTNU_SB (Astrid Laegrid, NTNU)
  • PAMGO_GAT (Michelle Gwinn)
  • PAMGO_MGG (Michelle Gwinn)
  • PseudoCAP (Fiona Brinkman)
  • Roslin_Institute
  • TIGR (Michelle Gwinn)
  • UniProt (same as UniProtKB?)


If you are part of any of these groups and would like to be the contact point, please email me so I can add you to the list. For the groups who do not reply, GO consortium will add itself as an editor of these annotations and will made changes to the annotations as necessary to ensure that the annotation meet our guidelines.

New Items

Contact Person(s) for GO Collaborations with External Groups

Update on Signaling Project

  • Signaling pathways claimed
    • Ca2+ signaling and fertilization - Penelope
    • MAPK - David
    • Wnt - Giulia, Helen, Kimberly

Minutes

  • On call: Chris, David H, Kimberly, Pascale, Paul T.

Annotation Qualifiers

  • Need to format documentation for github (generally)
  • Default qualifier can be chosen by the annotation group
    • Define the clear cut cases first
      • Use of regulates means that the mechanism is known
      • causally_upstream_of is a parent of regulates, so can be used for things that are upstream for which they may not be enough information to support a controlling, regulatory step
    • IMP annotations may get 'causally upstream of or within'
    • IDA annotations may get 'involved in'
  • Need to have guidelines for usage of new qualifiers
  • Need to move GAF docs from drupal to github
  • Need to confirm with consortium members
  • Need to message wider community
  • Still need a rollout plan!! Dates!!
    • What will be rolled out - github ticket for this so we actually move forward
    • Timeline may not be the same for all groups - that should be okay
    • Will there be problems if some annotations in the GAF have a qualifier and some don't?
      • There may not be a one-time switch for everyone, but by a certain date we will require qualifiers on all annotations
  • Pipeline from Noctua will still be for groups to consume the GPAD files, incorporate them into their GAF/GPAD submission
  • Need guidelines for consumers on how to use these qualifiers (both old and new qualifiers)

Working groups management on GitHub

Process to deal with stale annotations

  • Paul T. added some names
  • Other people in GO should take a look to see if they can add someone
  • Add this contact information to github
    • Add a contact field to the groups.yaml file
    • Add a field to the groups.yaml to indicate active/inactive
      • Need to also be clear on our policy for what happens to annotations supplied by groups that are inactive
        • What annotations stay and what annotations go?
        • Need to be able to delete annotations that are incorrect
        • If a group is no longer active, then curatorial ownership of the annotations is changed to GOC so updates can be made, as appropriate
    • https://github.com/geneontology/go-site/blob/master/metadata/groups.yaml